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Genome Scripts used in fungal comparative genomics
Perl Other
branch: master
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GO remove some defaults
R-gists compare GO stats in R
RNA-Seq separate cufflinks files into pairwise compared set
analyses some analyses - may get move elsewhere - focused on polyA site
annotation warnings on
assembly allow for min N size as a parameter
cluster_scripts cluster script
comparative create circos links file from a mercator map file
conservation_profile handle pairwise and parameterize the gap size cutoff
data_format remove some Cryptococcus specific stuff
gbrowse_tools handle when the features are top mapped directly to mRNA derived prot…
gene_prediction get the long enough contigs for prediction runs
gff_tools case insensitive
metagenomics use Swissprot hits to classify taxonomy and bin reads/ORFs by this
mutant_mapping add gene info to the VCF
ncbi eutils script to query sra for strain IDs
phylogenetics cmdline format options
popgen some SNP density calcs by contig/scaff
seq add GC count tool
seqfeature summarize feature type lengths from a GFF3 file
short-read fix legend
small-RNA u1a10 prediction
splice-analyses new splicing test script
summary_plots partition dS data by recombo block (coprinus paper)
viz do normalization
.gitignore ignore tmpfiles
LICENSE added Artistic License 2.0
README clarify

README

This repository is for public scripts which do data formatting, collation, and analysis.

This is mainly Perl code for genome annotation and processing.

Jason Stajich
University of California, Riverside
jason.stajich [at] ucr.edu
http://lab.stajich.org
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